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工欲善其事,必先利其器! – 科研干货,DNA序列编辑软件

工欲善其事,必先利其器!对于搞分子生物学的朋友们来说,也不例外。相信很多同学在刚开始接触DNA、蛋白研究的时候,导师或者同学有建议用哪个软件来分析DNA序列,设计PCR引物,甚至构建质粒序列。市面上有很多DNA分析软件,以小编的经历就遇见过至少20种,有的软件来自官方,比如NCBI,而有的软件则是由小门小户的序列发烧友编写的。那么到底用哪个是最为妥当的呢?这个问题肯定是没有定论的。小编认为各个软件在功能上大同小异,都可以对序列进行导入、读取、修改、酶切分析、比对等基础处理。所以软件好不好用,完全取决于使用者的习惯。本文就稍稍的说一些小编认为算是好用的软件。

1、Geneious

这个软件算是小编用过的最好用的DNA和蛋白序列分析软件,如果满分是10分的话,小编要给它打11分。除了基本的查看、编辑和分析功能之外,还可以进行对指定序列进行文献搜索,小编认为最牛X的功能是自动识别和标注。我们拿到一段没有标注的序列,放眼望去全是A、T、C、G而已,并不能知道哪里是基因序列、哪里是启动子序列、亦或者哪里有抗生素抗性片段。 Geneious可以自动识别并且标注,省去了手动标注的麻烦。

但是Geneious是个付费软件。刚刚下载的时候可以试用一个月(那个月是小编最幸福的日子~~~~),过了试用期,很多功能会被禁掉,但整个软件还是可以运行,并且能用于查看序列的。所以条件好的研究组可以考虑考虑:D

主页网址:http://www.geneious.com/

2、ApE

ApE是一款免费软件,也是小编平时一直在用的DNA序列分析软件。小编感觉ApE就是矮矬穷版的Geneious。除了没有自动检索的功能和单调的界面外,其他功能和Geneious差不多。ApE是美国犹他大学的一个生物学教授(M.Wayne Davis)编写的,可以算得上是个良心作品,毕竟人家不收费嘛!ApE有一个小问题,在OSX Mavericks (Mac 10.9以上系统)上工作时有个大bug,当然在Windows上工作还是很流畅的。

下载链接:http://biologylabs.utah.edu/jorgensen/wayned/ape/

3、Artemis

Artemis是桑格中心(Sangercenter)推出的一款免费的序列查看和标注软件。我们知道现在数据库里很多的基因组序列都是由桑格中心负责测序并且标注的,他们的研究人员就是用这个软件对基因组中的每个基因片段进行标注的。毕竟这是一个纯标注型软件,可能在质粒序列构建等功能上不如上面提到的两款软件。

下载链接:http://www.sanger.ac.uk/resources/software/artemis/#download

4、FastPCR

FastPCR其实是专门用来设计PCR引物的软件,也是免费的。小编个人喜欢灵活地设计引物,所以从来都是手动设计,并非使用软件。但小编认为对刚接触PCR的童鞋们来说,这款软件可以试一试。FastPCR操作界面很简单,导入DNA序列后就可以按自己的要求设计一定长度的引物。更人性化的一个功能是可以做in silico PCR(电脑模拟PCR),使用你自己设计的引物和各种规定的参数去构建一个虚拟的PCR反应,然后看看反应结果如何。对PCR新手来说,还是很有帮助的。

下载链接:http://www.primerdigital.com/fastpcr.html?page=35

5、SeqVert

SeqVert是一款很方便的文件格式转换器,也是免费的。序列文件的格式多种多样,有.fasta或者.gb或者.asn1 等等,文件之间的转化就异常重要。如果你使用的软件可以识别许多文件格式,那么格式转换器也不见得有那么重要了。ApE就可以识别好几种序列文件,所以小编在平时也很少用到文件格式转换器。

下载链接:http://genestudio.com/seqverter

6、SMS

有的童鞋可能不太喜欢用软件,那么有一些序列分析网站也是不错的选择。SMS (SequenceManipulation Suite) 是一个有60多种序列分析功能的站点。基本上PC端的序列分析软件的功能这个站点都有,所用的功能都一目了然,操作起来也是十分方便。不好的一点估计就是,要联网才能用,毕竟别人是个网站啊!

网址: http://www.bioinformatics.org/sms2/index.html

7、Benchling

Benchling算得上是网页版的Geneious了,各种序列编辑和分析的功能都有,而且使用起来十分方便。Benchling甚至可以计算培养皿上的菌落数量。Benchling的基础功能是全部免费的,需要用邮箱注册用户才能使用。不得不说,Benchling上做出来的质粒图确实是好看。由于是网页程序,所以只有联网才可以使用。

网址:https://benchling.com/

今天关于DNA序列分析软件就说这么多,希望能有帮到一些同学。在未来的文章中,小编还会介绍一些蛋白序列分析软件,蛋白结构查看软件等等。



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